9H5W | pdb_00009h5w

X-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from adenylate kinase (AK) - not visible in the structure model

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9H5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	substrate co-crystallized MLSTLAKRF/ASGKKDRM 0.1 M MES buffer [pH 5.0], 2.4 M ammonium sulfate, 0.2 mM n-dodecylmaltoside

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.788	α = 90
b = 114.442	β = 90
c = 124.633	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	RAYONIX MX-225		2014-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	48	99.9	0.126	0.141	0.062	0.997	11.8	5		85304

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.04		99.9	1.859	2.072	0.903	0.327		5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2	48	80910	4305	99.81	0.20227	0.2009	0.2011	0.22853	0.2285	RANDOM	39.272

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.16			-1.12		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.401
r_dihedral_angle_3_deg	15.502
r_dihedral_angle_4_deg	15.259
r_long_range_B_refined	7.503
r_dihedral_angle_1_deg	6.387
r_mcangle_it	3.805
r_scbond_it	3.745
r_mcbond_it	2.624
r_angle_refined_deg	1.593
r_chiral_restr	0.107
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6381
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	93

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction